NetCTL 1.2 Server

NetCTL 1.2 server predicts CTL epitopes in protein sequences. The current version 1.2 is an update to the version
1.0. The version 1.2 expands the MHC class I binding predicition to 12 MHC supertypes including the supertypes
A26 and B39.
The accuracy of the MHC class I peptide binding affinity is significantly improved compared to the earlier version.
Also the
prediction of proteasonal cleavage has been improved and is now identical to the predictions obtained by the
NetChop-3.0 server. The updated version has been trained on
a set of 886 known MHC class I ligands.

NOTE. On Aug 16 2006 a minor update to the server has been implemented improving the prediction accuracy for MHC
binding. The earlier version of the NetCTL 1.2 server (1.2 beta) is available via the versions history for the
server.

View the version history of this server.
All the previous versions are available on line, for comparison and
reference.

The MHC peptide binding is predicted using neural networks trained as described for the
NetMHC server. The proteasome cleavage
event is predicted using the version of the NetChop neural networks trained on C terminals
of known CTL epitopes as describe for the
NetChop-3.0 server. The TAP transport
efficiency is predicted using the weight matrix based method describe by
Peters et al.

The server includes predictions of MHC/peptide binding for 12 MHC class I supertypes. The output from the
neural network predicting MHC/peptide binding is a log transformed value related to the IC50 values in
nM units. For details on the transformation please see
output format.

The scores from the three individual prediction methods are integrated as a weighted sum with a relative
weight on peptide/MHC binding of 1. Different thresholds for the integrated score can be translated into
sensitivity/specificity values. In a large benchmark calculate containing more than 800 known MHC class I ligands
the following relations were found

PORTABLE VERSION

Would you prefer to run NetCTL at your own site? NetCTL 1.2 is available
as a stand-alone software package, with the same functionality as the service
above. Ready-to-ship packages exist for the most common UNIX platforms. There
is a
download page
for academic users; other users are requested to contact CBS Software Package
Manager at software@cbs.dtu.dk.

GETTING HELP

Scientific problems:
Technical problems:

This file was last modified Tuesday 17th 2015f November 2015 09:20:10 GMT